The magnitude and temporal variability of mineral dust deposition and its associated Fe and Mn inputs to coastal waters of the California Current System (CCS) has been scarcely investigated. Here we report a 5 year time series (April 2010 to December 2014) of mineral dust (Fdust), Fe (FFe), and Mn (FMn) fluxes to the coastal zone of the southern CCS. Atmospheric deposition displayed a strong seasonal trend, with lowest Fdust, FFe, and FMn during the warm season (May–October), a period dominated by strong moisture‐laden winds of oceanic origin. In contrast, the highest Fdust, FFe, and FMn were recorded during the cool season (November–April), a period characterized by strong winds devoid of moisture coming from the mainland. Our analysis suggests that Santa Ana Wind events could contribute with ∼15%, 20%, and 24%, respectively, to the total annual input of dust, Fe and Mn to the region. Besides, atmospheric soluble Fe inputs are equivalent to between 11% (warm season) and 35% (cool season) of the dissolved Fe supplied by upwelling. Our calculations indicate that atmospheric Fe deposition could explain between ∼5% (warm season) and 15% (cool season) of primary production reported for the southern CCS, suggesting that this route could also be an important input of Fe for primary producers in this region. Finally, the average Fdust, FFe, and FMn for the cool seasons showed a positive interannual trend that was significantly correlated with an intensification of drought conditions over the period 2010–2014 in northwest of Mexico and southwest of the United States.